R: Genomic Data Retrieval

# Genomic Data Retrieval

## Documentation for package ‘biomartr’ version 1.0.7

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

biomartr-package | Genomic Data Retrieval
biomart | Main BioMart Query Function
biomartr | Genomic Data Retrieval
cachedir | Get directory to store back end files like kingdom summaries etc
cachedir_set | Set directory to store back end files like kingdom summaries etc
check_annotation_biomartr | Check whether an annotation file contains outlier lines
download.database | Download a NCBI Database to Your Local Hard Drive
download.database.all | Download all elements of an NCBI databse
ensembl_divisions | List all available ENSEMBL divisions
get.ensembl.info | Helper function to retrieve species information from the ENSEMBL API
getAssemblyStats | Genome Assembly Stats Retrieval
getAttributes | Retrieve All Available Attributes for a Specific Dataset
getBio | A wrapper to all bio getters, selected with 'type' argument
getBioSet | Generic Bio data set extractor
getCDS | Coding Sequence Retrieval
getCDSSet | CDS retrieval of multiple species
getCollection | Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats
getCollectionSet | Retrieve a Collection: Genome, Proteome, CDS, RNA, GFF, Repeat Masker, AssemblyStats of multiple species
getDatasets | Retrieve All Available Datasets for a BioMart Database
getENSEMBL | Download sequence or annotation from ENSEMBL
getENSEMBL.gtf | Helper function for retrieving gtf files from ENSEMBL
getENSEMBL.Seq | Helper function for retrieving biological sequence files from ENSEMBL
getENSEMBLGENOMESInfo | Retrieve ENSEMBLGENOMES info file
getENSEMBLInfo | Retrieve ENSEMBL info file
getFilters | Retrieve All Available Filters for a Specific Dataset
getGenome | Genome Retrieval
getGENOMEREPORT | Retrieve NCBI GENOME_REPORTS file
getGenomeSet | Genome Retrieval of multiple species
getGFF | Genome Annotation Retrieval (GFF3)
getGFFSet | GFF retrieval of multiple species
getGO | Gene Ontology Query
getGroups | Retrieve available groups for a kingdom of life (only available for NCBI RefSeq and NCBI Genbank)
getGTF | Genome Annotation Retrieval (GTF)
getKingdomAssemblySummary | Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms
getKingdoms | Retrieve available kingdoms of life
getMarts | Retrieve information about available Ensembl Biomart databases
getMetaGenomeAnnotations | Retrieve annotation *.gff files for metagenomes from NCBI Genbank
getMetaGenomes | Retrieve metagenomes from NCBI Genbank
getMetaGenomeSummary | Retrieve the assembly_summary.txt file from NCBI genbank metagenomes
getProteome | Proteome Retrieval
getProteomeSet | Proteome retrieval of multiple species
getReleases | Retrieve available database releases or versions of ENSEMBL
getRepeatMasker | Repeat Masker Retrieval
getRNA | RNA Sequence Retrieval
getRNASet | RNA Retrieval of multiple species
getSummaryFile | Helper function to retrieve the assembly_summary.txt file from NCBI
getUniProtInfo | Get uniprot info from organism
getUniProtSTATS | Retrieve UniProt Database Information File (STATS)
is.genome.available | Check Genome Availability
listDatabases | Retrieve a List of Available NCBI Databases for Download
listGenomes | List All Available Genomes either by kingdom, group, or subgroup
listGroups | List number of available genomes in each taxonomic group
listKingdoms | List number of available genomes in each kingdom of life
listMetaGenomes | List available metagenomes on NCBI Genbank
listNCBIDatabases | Retrieve a List of Available NCBI Databases for Download
meta.retrieval | Perform Meta-Genome Retrieval
meta.retrieval.all | Perform Meta-Genome Retrieval of all organisms in all kingdoms of life
organismAttributes | Retrieve Ensembl Biomart attributes for a query organism
organismBM | Retrieve Ensembl Biomart marts and datasets for a query organism
organismFilters | Retrieve Ensembl Biomart filters for a query organism
read_assemblystats | Import Genome Assembly Stats File
read_cds | Import CDS as Biostrings or data.table object
read_genome | Import Genome Assembly as Biostrings or data.table object
read_gff | Import GFF File
read_proteome | Import Proteome as Biostrings or data.table object
read_rm | Import Repeat Masker output file
read_rna | Import RNA as Biostrings or data.table object
refseqOrganisms | Retrieve All Organism Names Stored on refseq
summary_cds | Retrieve summary statistics for a coding sequence (CDS) file
summary_genome | Retrieve summary statistics for a genome assembly file